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Journal Articles

Coalescence of liquid or gel-like DNA-encapsulating microdroplets

Takashi Nishio, Helmut Schiessel
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 134904 (2024)
https://doi.org/10.1063/5.0223951
Published: October 2024
View article titled, Coalescence of liquid or gel-like DNA-encapsulating microdroplets
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Journal Articles

In silico study of DNA mononucleotide self-assembly

Mattia Trapella, Tommaso Bellini, Cristiano De Michele
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 134905 (2024)
https://doi.org/10.1063/5.0226019
Published: October 2024
View article titled, <em>In silico</em> study of DNA mononucleotide self-assembly
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Journal Articles

DeepLNE++ leveraging knowledge distillation for accelerated multi-state path-like collective variables

Thorben Fröhlking, Valerio Rizzi, Simone Aureli, Francesco Luigi Gervasio
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 114102 (2024)
https://doi.org/10.1063/5.0226721
Published: September 2024
View article titled, DeepLNE++ leveraging knowledge distillation for accelerated multi-state path-like collective variables
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Journal Articles

Simulating temperature and tautomeric effects for vibrationally resolved XPS of biomolecules: Combining time-dependent and time-independent approaches to fingerprint carbonyl groups

Minrui Wei, Junxiang Zuo, Guangjun Tian, Weijie Hua
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 104303 (2024)
https://doi.org/10.1063/5.0224090
Published: September 2024
View article titled, Simulating temperature and tautomeric effects for vibrationally resolved XPS of biomolecules: Combining time-dependent and time-independent approaches to fingerprint carbonyl groups
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Journal Articles

Hindered intermolecular stacking of anti-parallel telomeric G-quadruplexes

Luca Bertini, Valeria Libera, Sara Catalini, Giorgio Schirò, Andrea Orecchini, Renzo Campanella, Valentina Arciuolo, Bruno Pagano, Caterina Petrillo, Cristiano De Michele, Lucia Comez, Alessandro Paciaroni
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 105101 (2024)
https://doi.org/10.1063/5.0225371
Published: September 2024
View article titled, Hindered intermolecular stacking of anti-parallel telomeric G-quadruplexes
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Journal Articles

The effect of the loop on the thermodynamic and kinetic of single base pair in pseudoknot

Shuhao Zhang, Zhen Wang, Jie Qiao, Ting Yu, Wenbing Zhang
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 085105 (2024)
https://doi.org/10.1063/5.0216593
Published: August 2024
View article titled, The effect of the loop on the thermodynamic and kinetic of single base pair in pseudoknot
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Journal Articles

Origins of fine structure in DNA melting curves

Arevik V. Asatryan, Albert S. Benight, Artem V. Badasyan
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 055103 (2024)
https://doi.org/10.1063/5.0213526
Published: August 2024
View article titled, Origins of fine structure in DNA melting curves
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Journal Articles

Delayed fragmentation of isolated nucleobases induced by MeV ions

T. Nakao, R. Takasu, H. Tsuchida, M. Saito, T. Majima
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 054302 (2024)
https://doi.org/10.1063/5.0215222
Published: August 2024
View article titled, Delayed fragmentation of isolated nucleobases induced by MeV ions
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Journal Articles

ANNaMo: Coarse-grained modeling for folding and assembly of RNA and DNA systems

F. Tosti Guerra, E. Poppleton, P. Šulc, L. Rovigatti
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 205102 (2024)
https://doi.org/10.1063/5.0202829
Published: May 2024
View article titled, ANNaMo: Coarse-grained modeling for folding and assembly of RNA and DNA systems
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Journal Articles

Plasmon–emitter coupling in cytosine-rich hairpin DNA-templated silver nanoclusters: Thermal reversibility, white light emission, and dynamics inside live cells

Subhajit Chakraborty, Srikrishna Pramanik, Shashi Shekhar, Saptarshi Mukherjee
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 154303 (2024)
https://doi.org/10.1063/5.0200544
Published: April 2024
View article titled, Plasmon–emitter coupling in cytosine-rich hairpin DNA-templated silver nanoclusters: Thermal reversibility, white light emission, and dynamics inside live cells
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Includes: Supplementary data
Journal Articles

Three-metal ion mechanism of cross-linked and uncross-linked DNA polymerase β: A theoretical study

Wen-Ting Chu, Zucai Suo, Jin Wang
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 155101 (2024)
https://doi.org/10.1063/5.0200109
Published: April 2024
View article titled, Three-metal ion mechanism of cross-linked and uncross-linked DNA polymerase β: A theoretical study
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Includes: Supplementary data
Journal Articles

Erratum: “The quaternary question: Determining allostery in spastin through dynamics classification learning and bioinformatics” [J. Chem. Phys. 158, 125102 (2023)]

Maria S. Kelly, Amanda C. Macke, Shehani Kahawatte, Jacob E. Stump, Abigail R. Miller, Ruxandra I. Dima
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 149901 (2024)
https://doi.org/10.1063/5.0208392
Published: April 2024
View article titled, Erratum: “The quaternary question: Determining allostery in spastin through dynamics classification learning and bioinformatics” [J. Chem. Phys. 158, 125102 (2023)]
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Includes: Supplementary data
Journal Articles

Base pair compositional variability influences DNA structural stability and tunes hydration thermodynamics and dynamics

Brataraj Ghosh, Sarbajit Layek, Dhananjay Bhattacharyya, Neelanjana Sengupta
Journal: The Journal of Chemical Physics
J. Chem. Phys. 159, 095101 (2023)
https://doi.org/10.1063/5.0154977
Published: September 2023
View article titled, Base pair compositional variability influences DNA structural stability and tunes hydration thermodynamics and dynamics
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Includes: Supplementary data
Journal Articles

Hyper Rayleigh scattering from DNA nucleotides in aqueous solution

Christian Jonin, Maksymilian Dereniowski, Estelle Salmon, Csilla Gergely, Katarzyna Matczyszyn, Pierre-François Brevet
Journal: The Journal of Chemical Physics
J. Chem. Phys. 159, 054303 (2023)
https://doi.org/10.1063/5.0155821
Published: August 2023
View article titled, Hyper Rayleigh scattering from DNA nucleotides in aqueous solution
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Includes: Supplementary data
Journal Articles

Dynamics of single-base editing: Theoretical analysis

Vardan Hoviki Vardanyan, Qian Wang, Anatoly B. Kolomeisky
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 245101 (2023)
https://doi.org/10.1063/5.0157193
Published: June 2023
View article titled, Dynamics of single-base editing: Theoretical analysis
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Journal Articles

High-performance strategies for the recent MRSF-TDDFT in GAMESS

Konstantin Komarov, Vladimir Mironov, Seunghoon Lee, Buu Q. Pham, Mark S. Gordon, Cheol Ho Choi
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 194105 (2023)
https://doi.org/10.1063/5.0148005
Published: May 2023
View article titled, High-performance strategies for the recent MRSF-TDDFT in GAMESS
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Includes: Supplementary data
Journal Articles

The quaternary question: Determining allostery in spastin through dynamics classification learning and bioinformatics

Maria S. Kelly, Amanda C. Macke, Shehani Kahawatte, Jacob E. Stump, Abigail R. Miller, Ruxandra I. Dima
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 125102 (2023)
https://doi.org/10.1063/5.0139273
Published: March 2023
View article titled, The quaternary question: Determining allostery in spastin through dynamics classification learning and bioinformatics
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Includes: Supplementary data
Journal Articles

Fractionation factors reveal hidden frustration in an ancient allosteric module

Bryan VanSchouwen, Leonardo Della Libera, Giuseppe Melacini
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 121101 (2023)
https://doi.org/10.1063/5.0139510
Published: March 2023
View article titled, Fractionation factors reveal hidden frustration in an ancient allosteric module
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Includes: Supplementary data
Journal Articles

Nucleic acid folding simulations using a physics-based atomistic free energy model

Chi H. Mak
Journal: The Journal of Chemical Physics
J. Chem. Phys. 156, 174114 (2022)
https://doi.org/10.1063/5.0086304
Published: May 2022
View article titled, Nucleic acid folding simulations using a physics-based atomistic free energy model
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Journal Articles

Can one detect intermediate denaturation states of DNA sequences by following the equilibrium open–close dynamic fluctuations of a single base pair?

Keerti Chauhan, Amit Raj Singh, Sanjay Kumar, Rony Granek
Journal: The Journal of Chemical Physics
J. Chem. Phys. 156, 164907 (2022)
https://doi.org/10.1063/5.0088109
Published: April 2022
View article titled, Can one detect intermediate denaturation states of DNA sequences by following the equilibrium open–close dynamic fluctuations of a single base pair?
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Includes: Supplementary data